a test error when I use ElmerSolver

[zhang liangfu]

Hi everyone!

i have a problem with ElmerSolver.i follow this website viewtopic.php?f=2&t=3653
But ,when I test ElmerSolver model ,I come across an error ElmerSlover:symbol look up eooer:/usr/lib/libmpi_f77.so.1:undefined symbol : opal_uses_threads

[annier]

Hi Mr. Zhang,
I guess you had some things related to OpenMPI during installation. Please make sure that Elmer compilation finds the path to mpi as described in page 2 of the link you have mentioned above.
For further illustration of your query, you can attach your installation and compilation log in this forum.
I hope for your reply.

Yours
Anil Kunwar

[zhang liangfu]

Hi MR.Anil,

Thank you for your reply. I install an openmpi and I allocate the openmpi path via "--with-mpi-inc-dir=/usr/include/openmpi" .but when It compiles,the "fem" module log as follows.I can make sure that the other parts are sucessfully installed,I do it one by one .

zlf@zlf-ThinkPad-T420:~/elmerfem/fem$ ./configure --prefix="$ELMER_HOME" --with-tcltk="-ltcl8.4 -ltk8.4" --with-mpi-inc-dir=/usr/include/mpich
checking build system type... x86_64-unknown-linux-gnu
checking host system type... x86_64-unknown-linux-gnu
checking target system type... x86_64-unknown-linux-gnu
checking for a BSD-compatible install... /usr/bin/install -c
checking whether build environment is sane... yes
checking for a thread-safe mkdir -p... /bin/mkdir -p
checking for gawk... no
checking for mawk... mawk
checking whether make sets $(MAKE)... yes
checking whether to enable maintainer-specific portions of Makefiles... no
checking for style of include used by make... GNU
checking for gcc... gcc
checking for C compiler default output file name... a.out
checking whether the C compiler works... yes
checking whether we are cross compiling... no
checking for suffix of executables...
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether gcc accepts -g... yes
checking for gcc option to accept ISO C89... none needed
checking dependency style of gcc... gcc3
checking for special C compiler options needed for large files... no
checking for _FILE_OFFSET_BITS value needed for large files... no
checking for ftello... yes
checking for fseeko... yes
checking for answer to meaning of life... 42
checking for default compilation flags... optimized
checking whether we are using the GNU C compiler... (cached) yes
checking whether gcc accepts -g... (cached) yes
checking for gcc option to accept ISO C89... (cached) none needed
checking dependency style of gcc... (cached) gcc3
checking for xlC... no
checking for pathCC... no
checking for icc... no
checking for CC... no
checking for g++... g++
checking whether we are using the GNU C++ compiler... yes
checking whether g++ accepts -g... yes
checking dependency style of g++... gcc3
checking for gfortran... gfortran
checking whether we are using the GNU Fortran compiler... yes
checking whether gfortran accepts -g... yes
checking for gfortran... gfortran
checking whether we are using the GNU Fortran 77 compiler... yes
checking whether gfortran accepts -g... yes
checking for ranlib... ranlib
checking for ar... ar
checking for ar flags... cru
checking whether we are using the Microsoft C compiler... no
checking for /lib/cpp... yes
checking for C++ linker flags... checking how to run the C preprocessor... /lib/cpp
checking for grep that handles long lines and -e... /bin/grep
checking for egrep... /bin/grep -E
checking for ANSI C header files... yes
checking for sys/types.h... yes
checking for sys/stat.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for memory.h... yes
checking for strings.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for unistd.h... yes
checking for 64 bit compilation flags... let's see what happens
checking for 64 bit CFLAGS... -m64 -fPIC
checking for 64 bit FCFLAGS... -m64 -fPIC
checking for 64 bit CXXFLAGS... -m64 -fPIC
checking for 64 bit FFLAGS... -m64 -fPIC
checking for void*... yes
checking size of void*... 8
checking to see if we got 64 bits... oh yes
checking how to get verbose linking output from gfortran... -v
checking for Fortran 77 libraries of gfortran... -L/usr/lib/gcc/x86_64-linux-gnu/4.8 -L/usr/lib/gcc/x86_64-linux-gnu/4.8/../../../x86_64-linux-gnu -L/usr/lib/gcc/x86_64-linux-gnu/4.8/../../../../lib -L/lib/x86_64-linux-gnu -L/lib/../lib -L/usr/lib/x86_64-linux-gnu -L/usr/lib/../lib -L/usr/lib/gcc/x86_64-linux-gnu/4.8/../../.. -lgfortran -lm -lquadmath
checking for dummy main to link with Fortran 77 libraries... none
checking for Fortran 77 name-mangling scheme... lower case, underscore, no extra underscore
checking how to get verbose linking output from gfortran... -v
checking for Fortran libraries of gfortran... -L/usr/lib/gcc/x86_64-linux-gnu/4.8 -L/usr/lib/gcc/x86_64-linux-gnu/4.8/../../../x86_64-linux-gnu -L/usr/lib/gcc/x86_64-linux-gnu/4.8/../../../../lib -L/lib/x86_64-linux-gnu -L/lib/../lib -L/usr/lib/x86_64-linux-gnu -L/usr/lib/../lib -L/usr/lib/gcc/x86_64-linux-gnu/4.8/../../.. -lgfortran -lm -lquadmath
checking for dummy main to link with Fortran libraries... none
checking for Fortran name-mangling scheme... lower case, underscore, no extra underscore
checking for Fortran char* mangling scheme... char_ptr
checking if fortran implements CONTIGUOUS attribute... yes
checking if fortran implements allocatable character strings... yes
checking for fortran intrinsic etime... found
checking for fortran intrinsic flush... found
checking for shl_load in -ldld... no
checking for shl_load... no
checking for shl_findsym... no
checking for dlopen in -ldl... yes
checking for dlopen... yes
checking for dlsym... yes
checking for dlerror... yes
checking for dlclose... yes
checking for mpi-directory...
checking for mpi-lib-directory...
checking for mpi-inc-directory... /usr/include/mpich
checking for mpi-library...
checking for mpi-include...
checking for compilation of an MPI program... seems ok
checking for mpf90... no
checking for mpxlf90... no
checking for saxpy_... no
checking for ATL_xerbla in -latlas... no
checking for saxpy_ in -lblas... yes
checking for daxpy_ in -ldaxpy... no
checking for saxpy_ in -lcxml... no
checking for saxpy_ in -ldxml... no
checking for saxpy_ in -lscs... no
checking for saxpy_ in -lcomplib.sgimath... no
checking for saxpy_ in -lblas... (cached) yes
checking for saxpy_ in -lessl... no
checking for saxpy_ in -lessl... (cached) no
checking for saxpy_ in -lblas... (cached) yes
checking for cheev_... no
checking for cheev_ in -llapack... yes
checking for huti_d_gmres_ in -lhuti... yes
checking for eio_init_ in -leiof... yes
checking for dseupd_ in -larpack... yes
checking for pdneupd_ in -lparpack... no
configure: WARNING: No parallel arpack found.
checking for HYPRE_IJMatrixCreate in -lHYPRE_IJ_mv... yes
checking for dmumps_ in -ldmumps... no
checking for dmumps_ in -ldmumps... (cached) no
configure: WARNING: MUMPS not found, some functionaly will be disabled.
checking for umfpack_di_defaults in -lumfpack... yes
checking for mtc_init in -lmatc... yes
checking for main in -lm... yes
configure: error: The MPI version needs parpack. Disabling MPI.

[annier]

Hi Mr. Zhang,
here is a similar post related to your topic:
http://comments.gmane.org/gmane.comp.cl ... .user/2274

Yours
Anil Kunwar

[annier]

Hi Mr. Zhang,
Steps:
1. Install openmpi and find where it is:
(In my context it is installed in /usr/lib/ directory)

2.Inside openmpi, there is include directory with .h files. you need to make this include directory of openmpi available to the path of Elmer through /usr/include/ directory by creating its symlink.

Code: Select all

$sudo -s

Code: Select all

#ln -s /usr/lib/openmpi/include/  /usr/include/mpi

3. Now the installation process can access openmpi of /usr/lib/ by going through /usr/include/. symlink is like desktop shortcut in windows.

4. Your configuration script will look like this for fem module

Code: Select all

./configure --prefix="$ELMER_HOME" --with-tcltk="-ltcl8.4 -ltk8.4" --with-mpi-inc-dir=/usr/include/mpi

previously you have been using /usr/include/mpich.


Yours
Anil Kunwar

[zhang liangfu]

Hi MR Anil,
I followed your advice and the "mpi problem" is solved .But I encountered a new problem ,the problem as follows:
I search on the Internet ,I find some one else run into the same problem viewtopic.php?f=2&t=2396
Unfortunately,the problem is not solved, I am sure I install the "hutiter module" but I am not sure this huti is the same thing with the "hutiter module"
I am ver sorry to trouble you many times.
zlf@zlf-ThinkPad-T420:~/elmerfem/fem$ ./configure --prefix="$ELMER_HOME" --with-tcltk="-ltcl8.4 -ltk8.4" --with-mpi-inc-dir=/usr/include/mpi
checking build system type... x86_64-unknown-linux-gnu
checking host system type... x86_64-unknown-linux-gnu
checking target system type... x86_64-unknown-linux-gnu
checking for a BSD-compatible install... /usr/bin/install -c
checking whether build environment is sane... yes
checking for a thread-safe mkdir -p... /bin/mkdir -p
checking for gawk... no
checking for mawk... mawk
checking whether make sets $(MAKE)... yes
checking whether to enable maintainer-specific portions of Makefiles... no
checking for style of include used by make... GNU
checking for gcc... gcc
checking for C compiler default output file name... a.out
checking whether the C compiler works... yes
checking whether we are cross compiling... no
checking for suffix of executables...
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether gcc accepts -g... yes
checking for gcc option to accept ISO C89... none needed
checking dependency style of gcc... gcc3
checking for special C compiler options needed for large files... no
checking for _FILE_OFFSET_BITS value needed for large files... no
checking for ftello... yes
checking for fseeko... yes
checking for answer to meaning of life... 42
checking for default compilation flags... optimized
checking whether we are using the GNU C compiler... (cached) yes
checking whether gcc accepts -g... (cached) yes
checking for gcc option to accept ISO C89... (cached) none needed
checking dependency style of gcc... (cached) gcc3
checking for xlC... no
checking for pathCC... no
checking for icc... no
checking for CC... no
checking for g++... g++
checking whether we are using the GNU C++ compiler... yes
checking whether g++ accepts -g... yes
checking dependency style of g++... gcc3
checking for gfortran... gfortran
checking whether we are using the GNU Fortran compiler... yes
checking whether gfortran accepts -g... yes
checking for gfortran... gfortran
checking whether we are using the GNU Fortran 77 compiler... yes
checking whether gfortran accepts -g... yes
checking for ranlib... ranlib
checking for ar... ar
checking for ar flags... cru
checking whether we are using the Microsoft C compiler... no
checking for /lib/cpp... yes
checking for C++ linker flags... checking how to run the C preprocessor... /lib/cpp
checking for grep that handles long lines and -e... /bin/grep
checking for egrep... /bin/grep -E
checking for ANSI C header files... yes
checking for sys/types.h... yes
checking for sys/stat.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for memory.h... yes
checking for strings.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for unistd.h... yes
checking for 64 bit compilation flags... let's see what happens
checking for 64 bit CFLAGS... -m64 -fPIC
checking for 64 bit FCFLAGS... -m64 -fPIC
checking for 64 bit CXXFLAGS... -m64 -fPIC
checking for 64 bit FFLAGS... -m64 -fPIC
checking for void*... yes
checking size of void*... 8
checking to see if we got 64 bits... oh yes
checking how to get verbose linking output from gfortran... -v
checking for Fortran 77 libraries of gfortran... -L/usr/lib/gcc/x86_64-linux-gnu/4.8 -L/usr/lib/gcc/x86_64-linux-gnu/4.8/../../../x86_64-linux-gnu -L/usr/lib/gcc/x86_64-linux-gnu/4.8/../../../../lib -L/lib/x86_64-linux-gnu -L/lib/../lib -L/usr/lib/x86_64-linux-gnu -L/usr/lib/../lib -L/usr/lib/gcc/x86_64-linux-gnu/4.8/../../.. -lgfortran -lm -lquadmath
checking for dummy main to link with Fortran 77 libraries... none
checking for Fortran 77 name-mangling scheme... lower case, underscore, no extra underscore
checking how to get verbose linking output from gfortran... -v
checking for Fortran libraries of gfortran... -L/usr/lib/gcc/x86_64-linux-gnu/4.8 -L/usr/lib/gcc/x86_64-linux-gnu/4.8/../../../x86_64-linux-gnu -L/usr/lib/gcc/x86_64-linux-gnu/4.8/../../../../lib -L/lib/x86_64-linux-gnu -L/lib/../lib -L/usr/lib/x86_64-linux-gnu -L/usr/lib/../lib -L/usr/lib/gcc/x86_64-linux-gnu/4.8/../../.. -lgfortran -lm -lquadmath
checking for dummy main to link with Fortran libraries... none
checking for Fortran name-mangling scheme... lower case, underscore, no extra underscore
checking for Fortran char* mangling scheme... char_ptr
checking if fortran implements CONTIGUOUS attribute... yes
checking if fortran implements allocatable character strings... yes
checking for fortran intrinsic etime... found
checking for fortran intrinsic flush... found
checking for shl_load in -ldld... no
checking for shl_load... no
checking for shl_findsym... no
checking for dlopen in -ldl... yes
checking for dlopen... yes
checking for dlsym... yes
checking for dlerror... yes
checking for dlclose... yes
checking for mpi-directory...
checking for mpi-lib-directory...
checking for mpi-inc-directory... /usr/include/mpi
checking for mpi-library...
checking for mpi-include...
checking for compilation of an MPI program... seems ok
checking for mpf90... no
checking for mpxlf90... no
checking for saxpy_... no
checking for ATL_xerbla in -latlas... no
checking for saxpy_ in -lblas... yes
checking for daxpy_ in -ldaxpy... no
checking for saxpy_ in -lcxml... no
checking for saxpy_ in -ldxml... no
checking for saxpy_ in -lscs... no
checking for saxpy_ in -lcomplib.sgimath... no
checking for saxpy_ in -lblas... (cached) yes
checking for saxpy_ in -lessl... no
checking for saxpy_ in -lessl... (cached) no
checking for saxpy_ in -lblas... (cached) yes
checking for cheev_... no
checking for cheev_ in -llapack... yes
checking for huti_d_gmres_ in -lhuti... no
configure: error: Libhuti wasn't found
zlf@zlf-ThinkPad-T420:~/elmerfem/fem$ ./configure --prefix="$ELMER_HOME" --with-tcltk="-ltcl8.4 -ltk8.4" --with-mpi-inc-dir=/usr/include/mpi
checking build system type... x86_64-unknown-linux-gnu
checking host system type... x86_64-unknown-linux-gnu
checking target system type... x86_64-unknown-linux-gnu
checking for a BSD-compatible install... /usr/bin/install -c
checking whether build environment is sane... yes
checking for a thread-safe mkdir -p... /bin/mkdir -p
checking for gawk... gawk
checking whether make sets $(MAKE)... yes
checking whether to enable maintainer-specific portions of Makefiles... no
checking for style of include used by make... GNU
checking for gcc... gcc
checking for C compiler default output file name... a.out
checking whether the C compiler works... yes
checking whether we are cross compiling... no
checking for suffix of executables...
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether gcc accepts -g... yes
checking for gcc option to accept ISO C89... none needed
checking dependency style of gcc... gcc3
checking for special C compiler options needed for large files... no
checking for _FILE_OFFSET_BITS value needed for large files... no
checking for ftello... yes
checking for fseeko... yes
checking for answer to meaning of life... 42
checking for default compilation flags... optimized
checking whether we are using the GNU C compiler... (cached) yes
checking whether gcc accepts -g... (cached) yes
checking for gcc option to accept ISO C89... (cached) none needed
checking dependency style of gcc... (cached) gcc3
checking for xlC... no
checking for pathCC... no
checking for icc... no
checking for CC... no
checking for g++... g++
checking whether we are using the GNU C++ compiler... yes
checking whether g++ accepts -g... yes
checking dependency style of g++... gcc3
checking for gfortran... gfortran
checking whether we are using the GNU Fortran compiler... yes
checking whether gfortran accepts -g... yes
checking for gfortran... gfortran
checking whether we are using the GNU Fortran 77 compiler... yes
checking whether gfortran accepts -g... yes
checking for ranlib... ranlib
checking for ar... ar
checking for ar flags... cru
checking whether we are using the Microsoft C compiler... no
checking for /lib/cpp... yes
checking for C++ linker flags... checking how to run the C preprocessor... /lib/cpp
checking for grep that handles long lines and -e... /bin/grep
checking for egrep... /bin/grep -E
checking for ANSI C header files... yes
checking for sys/types.h... yes
checking for sys/stat.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for memory.h... yes
checking for strings.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for unistd.h... yes
checking for 64 bit compilation flags... let's see what happens
checking for 64 bit CFLAGS... -m64 -fPIC
checking for 64 bit FCFLAGS... -m64 -fPIC
checking for 64 bit CXXFLAGS... -m64 -fPIC
checking for 64 bit FFLAGS... -m64 -fPIC
checking for void*... yes
checking size of void*... 8
checking to see if we got 64 bits... oh yes
checking how to get verbose linking output from gfortran... -v
checking for Fortran 77 libraries of gfortran... -L/usr/lib/gcc/x86_64-linux-gnu/4.8 -L/usr/lib/gcc/x86_64-linux-gnu/4.8/../../../x86_64-linux-gnu -L/usr/lib/gcc/x86_64-linux-gnu/4.8/../../../../lib -L/lib/x86_64-linux-gnu -L/lib/../lib -L/usr/lib/x86_64-linux-gnu -L/usr/lib/../lib -L/usr/lib/gcc/x86_64-linux-gnu/4.8/../../.. -lgfortran -lm -lquadmath
checking for dummy main to link with Fortran 77 libraries... none
checking for Fortran 77 name-mangling scheme... lower case, underscore, no extra underscore
checking how to get verbose linking output from gfortran... -v
checking for Fortran libraries of gfortran... -L/usr/lib/gcc/x86_64-linux-gnu/4.8 -L/usr/lib/gcc/x86_64-linux-gnu/4.8/../../../x86_64-linux-gnu -L/usr/lib/gcc/x86_64-linux-gnu/4.8/../../../../lib -L/lib/x86_64-linux-gnu -L/lib/../lib -L/usr/lib/x86_64-linux-gnu -L/usr/lib/../lib -L/usr/lib/gcc/x86_64-linux-gnu/4.8/../../.. -lgfortran -lm -lquadmath
checking for dummy main to link with Fortran libraries... none
checking for Fortran name-mangling scheme... lower case, underscore, no extra underscore
checking for Fortran char* mangling scheme... char_ptr
checking if fortran implements CONTIGUOUS attribute... yes
checking if fortran implements allocatable character strings... yes
checking for fortran intrinsic etime... found
checking for fortran intrinsic flush... found
checking for shl_load in -ldld... no
checking for shl_load... no
checking for shl_findsym... no
checking for dlopen in -ldl... yes
checking for dlopen... yes
checking for dlsym... yes
checking for dlerror... yes
checking for dlclose... yes
checking for mpi-directory...
checking for mpi-lib-directory...
checking for mpi-inc-directory... /usr/include/mpi
checking for mpi-library...
checking for mpi-include...
checking for compilation of an MPI program... seems ok
checking for mpf90... no
checking for mpxlf90... no
checking for saxpy_... no
checking for ATL_xerbla in -latlas... no
checking for saxpy_ in -lblas... yes
checking for daxpy_ in -ldaxpy... no
checking for saxpy_ in -lcxml... no
checking for saxpy_ in -ldxml... no
checking for saxpy_ in -lscs... no
checking for saxpy_ in -lcomplib.sgimath... no
checking for saxpy_ in -lblas... (cached) yes
checking for saxpy_ in -lessl... no
checking for saxpy_ in -lessl... (cached) no
checking for saxpy_ in -lblas... (cached) yes
checking for cheev_... no
checking for cheev_ in -llapack... yes
checking for huti_d_gmres_ in -lhuti... no
configure: error: Libhuti wasn't found


lokking forward to you

yours sincerely zhang liangfu

[annier]

Hi Mr. Zhang,
Could you try with this:

Code: Select all

./configure --prefix="$ELMER_HOME"   \
 --with-tcltk="-ltcl8.4 -ltk8.4" \
 --with-mpi-inc-dir=/usr/include/mpi \
 --with-lhuti=$ELMER_HOME/lib/libhuti.a 

and reply with the result.

Notes:
1. Since fem module is dependent on libhuti.a which will be placed in $ELMER_HOME directory after hutiter module is installed, it is mandatory that we need to install hutiter module earlier than fem module.

• Code: Select all

  modules="matc umfpack mathlibs elmergrid meshgen2d eio hutiter fem"

  This is correct.

• Code: Select all

  modules="matc umfpack mathlibs elmergrid meshgen2d eio fem hutiter "

  Here, the compilation of fem takes place earlier than hutiter and the former may not get the libhutiter.a required for it.

2. If hutiter module has been installed successfully, then compilation of fem module will find the libhuti.a file along the path described in the above code. Now, we can understand why fem module is kept at the last of the modules.

Yours
Anil Kunwar

[zhang liangfu]

Hi Anil,
I do it as you say ,but the same error occurs as the last reply,"the mpi version needs parpack"the configure error as follows
zlf@zlf-ThinkPad-T420:~/elmerfem/fem$ ./configure --prefix="$ELMER_HOME" --with-tcltk="-ltcl8.4 -ltk8.4" --with-mpi=yes --with-mpi-dir=/usr/lib/openmpi --with-mpi-inc-dir=/usr/include/mpi
checking build system type... x86_64-unknown-linux-gnu
checking host system type... x86_64-unknown-linux-gnu
checking target system type... x86_64-unknown-linux-gnu
checking for a BSD-compatible install... /usr/bin/install -c
checking whether build environment is sane... yes
checking for a thread-safe mkdir -p... /bin/mkdir -p
checking for gawk... gawk
checking whether make sets $(MAKE)... yes
checking whether to enable maintainer-specific portions of Makefiles... no
checking for style of include used by make... GNU
checking for gcc... gcc
checking for C compiler default output file name... a.out
checking whether the C compiler works... yes
checking whether we are cross compiling... no
checking for suffix of executables...
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether gcc accepts -g... yes
checking for gcc option to accept ISO C89... none needed
checking dependency style of gcc... gcc3
checking for special C compiler options needed for large files... no
checking for _FILE_OFFSET_BITS value needed for large files... no
checking for ftello... yes
checking for fseeko... yes
checking for answer to meaning of life... 42
checking for default compilation flags... optimized
checking whether we are using the GNU C compiler... (cached) yes
checking whether gcc accepts -g... (cached) yes
checking for gcc option to accept ISO C89... (cached) none needed
checking dependency style of gcc... (cached) gcc3
checking for xlC... no
checking for pathCC... no
checking for icc... no
checking for CC... no
checking for g++... g++
checking whether we are using the GNU C++ compiler... yes
checking whether g++ accepts -g... yes
checking dependency style of g++... gcc3
checking for gfortran... gfortran
checking whether we are using the GNU Fortran compiler... yes
checking whether gfortran accepts -g... yes
checking for gfortran... gfortran
checking whether we are using the GNU Fortran 77 compiler... yes
checking whether gfortran accepts -g... yes
checking for ranlib... ranlib
checking for ar... ar
checking for ar flags... cru
checking whether we are using the Microsoft C compiler... no
checking for /lib/cpp... yes
checking for C++ linker flags... checking how to run the C preprocessor... /lib/cpp
checking for grep that handles long lines and -e... /bin/grep
checking for egrep... /bin/grep -E
checking for ANSI C header files... yes
checking for sys/types.h... yes
checking for sys/stat.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for memory.h... yes
checking for strings.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for unistd.h... yes
checking for 64 bit compilation flags... let's see what happens
checking for 64 bit CFLAGS... -m64 -fPIC
checking for 64 bit FCFLAGS... -m64 -fPIC
checking for 64 bit CXXFLAGS... -m64 -fPIC
checking for 64 bit FFLAGS... -m64 -fPIC
checking for void*... yes
checking size of void*... 8
checking to see if we got 64 bits... oh yes
checking how to get verbose linking output from gfortran... -v
checking for Fortran 77 libraries of gfortran... -L/usr/lib/gcc/x86_64-linux-gnu/4.8 -L/usr/lib/gcc/x86_64-linux-gnu/4.8/../../../x86_64-linux-gnu -L/usr/lib/gcc/x86_64-linux-gnu/4.8/../../../../lib -L/lib/x86_64-linux-gnu -L/lib/../lib -L/usr/lib/x86_64-linux-gnu -L/usr/lib/../lib -L/usr/lib/gcc/x86_64-linux-gnu/4.8/../../.. -lgfortran -lm -lquadmath
checking for dummy main to link with Fortran 77 libraries... none
checking for Fortran 77 name-mangling scheme... lower case, underscore, no extra underscore
checking how to get verbose linking output from gfortran... -v
checking for Fortran libraries of gfortran... -L/usr/lib/gcc/x86_64-linux-gnu/4.8 -L/usr/lib/gcc/x86_64-linux-gnu/4.8/../../../x86_64-linux-gnu -L/usr/lib/gcc/x86_64-linux-gnu/4.8/../../../../lib -L/lib/x86_64-linux-gnu -L/lib/../lib -L/usr/lib/x86_64-linux-gnu -L/usr/lib/../lib -L/usr/lib/gcc/x86_64-linux-gnu/4.8/../../.. -lgfortran -lm -lquadmath
checking for dummy main to link with Fortran libraries... none
checking for Fortran name-mangling scheme... lower case, underscore, no extra underscore
checking for Fortran char* mangling scheme... char_ptr
checking if fortran implements CONTIGUOUS attribute... yes
checking if fortran implements allocatable character strings... yes
checking for fortran intrinsic etime... found
checking for fortran intrinsic flush... found
checking for shl_load in -ldld... no
checking for shl_load... no
checking for shl_findsym... no
checking for dlopen in -ldl... yes
checking for dlopen... yes
checking for dlsym... yes
checking for dlerror... yes
checking for dlclose... yes
checking for mpi-directory... /usr/lib/openmpi
checking for mpi-lib-directory... /usr/lib/openmpi/lib
checking for mpi-inc-directory... /usr/include/mpi
checking for mpi-library...
checking for mpi-include...
checking for compilation of an MPI program... seems ok
checking for mpf90... no
checking for mpxlf90... no
checking for saxpy_... no
checking for ATL_xerbla in -latlas... no
checking for saxpy_ in -lblas... yes
checking for daxpy_ in -ldaxpy... no
checking for saxpy_ in -lcxml... no
checking for saxpy_ in -ldxml... no
checking for saxpy_ in -lscs... no
checking for saxpy_ in -lcomplib.sgimath... no
checking for saxpy_ in -lblas... (cached) yes
checking for saxpy_ in -lessl... no
checking for saxpy_ in -lessl... (cached) no
checking for saxpy_ in -lblas... (cached) yes
checking for cheev_... no
checking for cheev_ in -llapack... yes
checking for huti_d_gmres_ in -lhuti... yes
checking for eio_init_ in -leiof... yes
checking for dseupd_ in -larpack... yes
checking for pdneupd_ in -lparpack... no
configure: WARNING: No parallel arpack found.
checking for HYPRE_IJMatrixCreate in -lHYPRE_IJ_mv... yes
checking for dmumps_ in -ldmumps... no
checking for dmumps_ in -ldmumps... (cached) no
configure: WARNING: MUMPS not found, some functionaly will be disabled.
checking for umfpack_di_defaults in -lumfpack... yes
checking for mtc_init in -lmatc... yes
checking for main in -lm... yes
configure: error: The MPI version needs parpack. Disabling MPI.


I don't know how to solve it ,I search it everywhere, can you tell me what is your mating software ? I just don't know where I wrong.
looking forward to you
zhang liangfu

[annier]

Hi Mr. Zhang,
Regarding your configuration script:

Code: Select all

 ./configure --prefix="$ELMER_HOME" --with-tcltk="-ltcl8.4 -ltk8.4" --with-mpi=yes --with-mpi-dir=/usr/lib/openmpi --with-mpi-inc-dir=/usr/include/mpi 

there are 2 directions for mpi : one is openmpi and one is more mpi at 2 different locations. How did you configure like this? if the mpi at /usr/include is a symlink for openmpi, then i think only mentioning the /usr/include/ is ok.

Didn't you try for this?

Code: Select all

./configure --prefix="$ELMER_HOME"   \
--with-tcltk="-ltcl8.4 -ltk8.4" \
--with-mpi-inc-dir=/usr/include/mpi \
--with-lhuti=$ELMER_HOME/lib/libhuti.a 

Yours
Anil Kunwar

[annier]

Hi Mr. Zhang,
Try installing these dependencies first and start the installation of Elmer (fem module)

Code: Select all

$sudo apt-get install  libblas-dev liblapack-dev libatlas-dev libarpack2-dev \
libparpack2-dev libmpich2-dev libhypre-dev mpi-default-dev mpi-default-bin

or,

Code: Select all

$ sudo apt-get install libparpack2-dev

and each of the above as per requirement.

These are the name of the dependencies you need to have installed before installing the fem module of Elmer

Code: Select all

    Libs:
      BLAS                     
      LAPACK                   
      HYPRE                     -lHYPRE_Euclid -lHYPRE_parcsr_ls -lHYPRE_ParaSails -lHYPRE_IJ_mv
      UMFPACK                   -lumfpack -lamd
      ARPACK          -larpack
      PARPACK          -lparpack
      HUTI             -lhuti
      EIO             -leiof
      MPI                       -L/usr/lib/openmpi//lib
  

Out of them umfpack, eio and hutiter are included in the compile script (since they come along with the Elmer package). whereas it will be assumed that the others have been already installed in your Ubuntu machine before you start installing Elmer. So, ensure that your computer has these libraries installed. For now, the error is in not finding Parpack library. so, you need to install it using the above codes.


Yours
Anil Kunwar